Mass spectrometric data analyzing method, mass spectrometric data analyzing apparatus, mass spectrometric data analyzing program, and solution offering system

ABSTRACT

A main object is to cope with an unknown structure substance thereby to identify the structure of a parent ion highly precisely and to derive a supposed structure. A method for analyzing mass spectrometric data is disclosed, which: acquires mass spectrometric data on an ionized sample and dissociated ions dissociated from the sample as a parent ion; derives dissociated ion candidates by analyzing the molecular orbits on the candidates of the structures of the parent ion; and displays the analytical results of the parent ion candidates and the dissociated ion candidates and compares the data of the dissociated ion candidates and the data of dissociated ions actually measured, to evaluate the structures of the parent ion candidates.

The present application is a continuation of application Ser. No.10/253,481, filed Sep. 25, 2002, now U.S. Pat. No. 6,907,352, the entiredisclosure of which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to an analytical method for analyzing massspectrometric data, a mass spectrometric data analyzing apparatus, amassspectrometric data analyzing program, and a solution offering system.

2. Description of Related Art

There has been an increasing need for a mass spectrometer which has atandem mass spectrometric function to dissociate a substance (or aparent ion) to improve the identification precision of the substancefrom mass spectrometric data obtained by the mass spectrometer, and toperform further mass spectrometry of the dissociated ions. The methodfor identifying the parent ion and for deriving the supposed structureof the parent ion with the mass spectrometric data (i.e., MS data) ofthe parent ion and the mass spectrometric data (i.e., MS² data) of thedissociated ions is mainly classified into the following methods:

(1) A database retrieving method of the mass spectrometric data (i.e.,the MS data) of the parent ion;

(2) A database retrieving method of the mass spectrometric data (i.e.,the MS data and the MS² data) of the parent ion and the dissociatedions; and

(3) A method for suppositions based on the mass spectrometric data(i.e., the MS data and the MS² data) of the parent ion and thedissociated ions but not depending on the database.

On One example of the related art (2) is disclosed in JP-A-8-124519. Inthis disclosure, for the individual peaks of the mass spectrum or massspectrometric data, the candidates for the ion species corresponding tothe peak mass are extracted with reference to the peak database, and thecandidates for the eliminated radicals corresponding to the eliminationmass are extracted with reference to the elimination radical database.Moreover, the candidates for the parent ion are determined withreference to the structure constructing database which is stored withrules for constructing the parent ion from the dissociated ions and theeliminated radicals.

In an amino acid configuration analysis supporting software “SeqMS”developed by Ohsaka University, on the other hand, the related art (3)is exemplified by identifying about ten amino acid configurations ofpeptide without resorting to the database retrieval. This softwarederives the amino acid configuration candidates by the statisticalprocedures which are based on the graph theory using the weightingvalues of the dissociation probability determined empirically (orexperimentally) from the mass spectrometric data of the peptide ions andtheir dissociated ions.

When the database retrievals of the related arts (1) and (2) are used asthe method for identifying the parent ion and for deriving the supposedstructure of the parent ion by the mass spectrometric data (i.e., the MSdata) of the parent ion and the mass spectrometric data (i.e., the MS²data) of the dissociated ions, however, the parent ion is difficult toidentify, and the supposed structure is difficult to derive, because nodata is present in the database for a substance having an unknownstructure.

When the statistical processing based on the graph theory and theinformation processing of a numerical arrangement are performed as themethod without resorting to the database retrieval, as disclosed in therelated art (3), on the other hand, it is the current practice that theidentification precision of the parent ion is seriously lowered to onehalf or less.

Therefore, a main object of the present invention is to cope with anunknown structure substance thereby to identify the structure of aparent ion highly precisely and to derive a supposed structure.

SUMMARY OF THE INVENTION

As the means of the present invention for solving the aforementionedproblems, the structures of a parent ion or a sample and dissociatedions produced from the parent ion are derived precisely by acquiring themass spectrometric data of the parent ion and the dissociated ions andby performing a molecular orbit analysis by itself or in combinationwith molecular dynamic calculations or molecular kinetic calculations,upon the structure of the parent ion, as supposed from the massspectrometric data. Moreover, this means can be expanded to services foroffering the analytical result as a solution to a customer.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram showing a construction of a mass spectrometer or amass spectrometric data analyzing apparatus of the present invention;

FIG. 2 is a flow chart showing a mass spectrometric data analyzingmethod;

FIG. 3A is a diagram illustrating mass spectrometric data of a parention, and FIG. 3B is a diagram illustrating mass spectrometric data ofdissociated ions;

FIGS. 4A, 4B and 4C are diagrams illustrating analytical result screens;

FIG. 5A is an analytical result screen, FIG. 5B is a correspondingscreen, and FIG. 5C is an evaluation screen;

FIG. 6 is a ranking indication screen for indicating the analyticalresult;

FIG. 7 is a distribution indication screen for indicating the analyticalresult;

FIG. 8 is a strength indication screen for indicating the analyticalresult;

FIG. 9 is a signal indication screen for indicating the analyticalresult;

FIG. 10 is a diagram illustrating the dissociation procedures of thesample schematically noting the activation energy;

FIG. 11 is a diagram illustrating the dissociation procedures of thesample schematically noting the activation energy;

FIG. 12A illustrates the mass spectrometric data of the parent ionmeasured on reserpine, and FIG. 12B illustrates the mass spectrometricdata of the dissociated ions;

FIG. 13 is a diagram illustrating the most proton-bondable site in thereserpine areally;

FIG. 14 is a flow chart showing a mass spectrometric data analyzingmethod;

FIG. 15 is a diagram illustrating a structure of angiotensin;

FIG. 16 is a diagram showing a construction of a mass spectrometer or amass spectrometric data analyzing apparatus;

FIG. 17 is a flow chart showing a mass spectrometric data analyzingmethod;

FIG. 18 is a surface screen enumerating the configuration of an aminoacid in a table, and a pop-up screen illustrating a three-dimensionalstructure of a specific configuration;

FIG. 19 is a diagram showing a construction of a mass spectrometer or amass spectrometric data analyzing apparatus;

FIG. 20 is a diagram showing a construction of a mass spectrometer or amass spectrometric data analyzing apparatus;

FIG. 21 is a diagram showing a construction of a mass spectrometer or amass spectrometric data analyzing apparatus; and

FIG. 22 is a diagram for explaining a solution offering system to bemade by using the mass spectrometric data analyzing apparatus of thepresent invention.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

(First Embodiment)

A first embodiment of the present invention will be described in detailwith reference to the accompanying drawings.

FIG. 1 is a block diagram showing a construction of a mass spectrometeror a mass spectrometric data analyzing apparatus, and FIG. 2 is a flowchart showing a processing of the mass spectrometer.

The present embodiment is characterized in that a structure analysis ofa sample is performed: by operating at least one of the thermal,chemical and energetic properties of a structure supposed on the basisof the mass spectrometric result of the sample, by a molecular orbitanalysis; and by evaluating the validity of the supposed structure onthe basis of the operation result. This processing is performed by usinga mass spectrometer 24 shown in FIG. 1.

The mass spectrometer 24 or the mass spectrometric data analyzingapparatus includes: a data processing unit 12 for analyzing a molecularorbit analysis on the mass spectrometric data 1 measured on a sample tobe analyzed; and a display unit 13 for displaying the analytical result.The measurement of the mass spectrometric data is made by ionizing thesample, after pretreated in a pretreatment system 8 such as a liquidchromatograph, by the well-known method in an ionization unit 9, and bydetecting the ions dissociated according to the mass in a massspectrometric unit 10, by an ion detection unit 11. This massspectrometer 24 is generally controlled by a control unit 14. Thiscontrol unit 14 controls a series of mass spectrometric procedureincluding the pretreatment of the sample, the ionization of the sample,the transfer and incidence of the sample ion beam obtained by theionization, to and on the mass spectrometric unit 10, the massseparating procedure and the ion detection.

The mass spectrometric unit 10 may be provided with dissociation meansfor producing dissociated ions (or daughter ions) having smaller massnumbers by cleaving the ionized sample by a collision induceddissociation. The method for the mass spectrometry of the dissociatedions, too, by using the dissociation means is called the tandem massspectrometry (or the MS/MS analysis). According to this method,information on the molecules constructing the parent ion (or the sampleion) can be acquired to suppose the structure of the parent ion on theinformation. This dissociation means can be exemplified by a collisioncell. The collision cell is a device for producing the dissociated ionsby causing an inert gas such as helium used as a buffer gas to collideagainst specific sample ions. The collision induced dissociationphenomenon in a low-energy region, as caused by causing the buffer gassuch as the inert gas to collide against the parent ion, is thought asthe thermal dissociation phenomenon, i.e., the thermochemical reaction.As another example of the dissociation means, there can be enumerated adevice for producing the dissociated ions by irradiating with aninfrared ray. Here, the mass spectrometer 24 need not be provided withthe dissociation means when it uses only the method (the MS analysis) bywhich the sample is ionized and analyzed as it is. The followingdescription will be made with an assumption that the mass spectrometer24 includes the dissociation means and makes the tandem massspectrometry. Therefore, an ionized sample before being dissociatedshall be termed a parent ion.

The data processing unit 12 is constructed to include a CPU (CentralProcessing Unit), a ROM (Read Only Memory) and a RAM (Random AccessMemory), and identifies the parent ion by making the molecular orbitanalysis of the parent ion, as will be described, when the analyticprograms for the mass spectrometric data analysis are expanded/started.

The display unit 13 can be exemplified by a CRT (Cathode-Ray Tube)display or a liquid crystal display. The display unit 13 may also beanother means if it can display another data processing result to bemade by the data processing unit 12.

Examples of the mass spectrometric data 1, as obtained by such massspectrometer 24, of the parent ion and the dissociated ions areillustrated at FIGS. 3A and 3B. FIG. 3A illustrates the massspectrometric data 1 of the parent ion and that the parent ion has amass-to-charge ratio (as will be expressed by m/z) of 340 amu. FIG. 3Billustrates the mass spectrometric data 1 of the dissociated ionsobtained by causing the parent ion to collide thereby to dissociate it,and peaks are observed at locations of m/z=179 amu and m/z=310 amu. Thismeans that the dissociated ion of m/z=179 amu and the dissociated ion ofm/z=310 amu are produced from the parent ion of m/z=340 amu by thedissociation means of the mass spectrometric unit 10 shown in FIG. 1.

The present embodiment analyzes the structure of the parent ion on thebasis of the mass spectrometric data 1 obtained on such parent ion anddissociated ions. This analyzing procedure will be described withreference to the flow chart of FIG. 2. Here, the sample the structure ofwhich is to be analyzed as the parent ion is exemplified by either ahigh molecule relating to a living organism such as protein, peptide orsaccharides, or a low molecule having an unknown structure on asynthetic molecule such as a medicine. However, the sample should not belimited to those molecular weights or kinds.

First of all, at Step S1 of FIG. 2, the mass spectrometric data 1 on theparent ion are acquired by using the mass spectrometric unit 10. Thesemass spectrometric data 1 are obtained through a series of massspectrometric procedure and composed of the mass spectrometric data ofthe parent ion (as will be referred to “MS data 1 a” fordiscriminations) and the mass spectrometric data, as made by using thedissociation means, of the dissociated ions (as will also be referred to“MS² data 1 b” for discriminations).

At subsequent Step S2, the structure of the parent ion is estimated. Thesupposing method to be used here can be exemplified by a method forsupposing the structure from the preparing procedure of the sample and amethod for the user to make a coarse estimation on the basis of the massspectrometric data 1 of the parent ion. These methods may be replaced byor used together with a method for supposing the structure of the parention by processing a software to list up the conceivable structures ofthe parent ion as candidates on the basis of the MS data 1 a. Thesupposition of the structure of the parent ion at this stage is done forselecting the candidates for such procedures at and after Step S3 whichcharacterize the present embodiment and is desired to list up aplurality of structures. For an easier understanding, the descriptionwill be made on the case, in which a parent ion candidate 2 a having aplanar structure using molecular symbols shown in FIG. 4A is to beprocessed. It is desired that the parent ion candidate 2 a supposed isso displayed as a parent ion candidate screen 2 that its constructionmay be easily confirmed by the user.

On the structure of the parent ion candidate 2 a supposed at theaforementioned Step, the molecular orbit is analyzed at Step S 3 bycalculating at least one of the thermal, chemical and energeticproperties of the molecular structure. In the present embodiment, thestrength of interatomic bonds is taken up as the thermal, chemical andenergetic properties, and the data processing unit 12 shown in FIG. 1uses the molecular orbit analysis to operate the strength of theinteratomic bonds of the atoms constructing the parent ion candidate 2a.

The analytical result on the parent ion candidate 2 a is displayed atStep S4 in the display unit 13 (as referred to FIG. 1). The display ofthis case is exemplified by an analytical result screen 3, as shown inFIG. 4B. The analytical result screen 3 contains the stereoscopicstructure of the parent ion candidate 2 a, digits attached to apredetermined bonds, and texts 3 a explaining the digits. According tothis analytical result screen 3, it is easily understood from the texts3 a that the digits attached to the bonds indicate a bonding strength σ.It can also be judged that the bonds having smaller digits have a lowerbonding strength σ. Here, the bonding strength σ indicates only suchinteratomic bonds in relative values as have relative strengths at orless than a predetermined value, but may indicate them in absolutevalues or all bonds in relative values or absolute values. As in ananalytical result screen 4 shown in FIG. 4C, on the other hand, thebonding strengths σ may be ranked from the smaller one so that rankindications 4 a and 4 b indicating the ranks schematically may bedisplayed together with the stereoscopic structure of the parent ioncandidate 2 a. In this analytical result screen 4, the rank indication 4a of the lowest bonding strength σ and the rank indication 4 b of thesecond lowest bonding strength are shown to have the digits indicatingthe individual ranks and the drawings connecting the digits and thebonds, so that the portion of a weak bond can be quickly confirmed.

Here, the reason why the smaller two bonding strengths σ are selected isthat the structure of the parent ion is efficiently evaluated by notingthe dissociated ions of higher production probabilities because theprobability of those bonds being broken to produce the dissociated ionscan be deemed high. The number of bonding strengths σ to be noted isdifferent from the mass number and structure of the sample. It is,therefore, desirable that the noted number can be changed into one ormore by the procedure of the data processing unit 12 (as in thefollowing case in which the number of noted data to be indicated isplural). Moreover, the analytical result screens 3 and 4 may display theplanar structure of the parent ion candidate 2 a.

On the basis of the bonding strength σ obtained by the molecular orbitanalysis at Step S3, moreover, the dissociated ions, which can bepredicted when the parent ion candidate 2 a is dissociated into aplurality of ions, are derived as the dissociated ion candidates at StepS5. In this case, two peaks are obtained as the MS² data 1 b of thedissociated ions, as illustrated in FIG. 3B. Therefore, the dissociatedion candidates are derived assuming that the bonds are broken at twoportions of weak bonding strengths σ (i.e., the bonds specified by therank indication 4 a and the rank indication 4 b in FIG. 4C). Here, thederivations of the dissociated ion candidates are to specify thestructures of the dissociated ions at the data processing unit 12 shownin FIG. 1 and to calculate their mass-to-charge ratios (m/z).

The analytical results of the dissociated ion candidates are sodisplayed in the display unit 13 at Step S6 that the user may be easilyable to confirm their structures and m/z values and to grasp thederivation grounds. The display is exemplified by an analytical resultscreen 5 shown in FIG. 5A. In the analytical result screen 5, there aredisplayed dissociated ion candidates 5 a and 5 b which show the twodissociated ions derived. The dissociated ion candidate 5 a has astructure of the dissociated ion which is produced when the bond of thelowest bonding strength σ is broken, and is displayed in the analyticalresult screen 5 in relation to the m/z value and the derivation ground(i.e., the text “DISSOCIATED ION BY DISSOCIATIVE SITE No. 1”). Thedissociated ion candidate 5 b has a structure of the dissociated ionwhich is produced when the bond of the second lowest bonding strength σis broken, and is displayed in the analytical result screen 5 inrelation to the m/z value and the derivation ground (i.e., the text“DISSOCIATED ION BY DISSOCIATIVE SITE No. 2”).

By this procedure, there has been ended the structure analysis using themolecular orbit method on the parent ion candidate 2 a. At subsequentStep S7, the dissociated ion candidates 5 a and 5 b derived by thestructure analysis and the MS² data (as referred to FIG. 3B) or themeasured values of the dissociated ions are compared to output theresult as a corresponding screen 6 shown in FIG. 5B. This correspondingscreen 6 is a graph, in which the peaks of the m/z values of thedissociated ion candidates 5 a and 5 b derived by the analysis aredisplayed as the mass spectra over the peaks 6 a and 6 b of the measuredvalues of the mass spectra obtained as the MS² data 1 b, as shown inFIG. 3B. In this Figure, the m/z values of the measured values and them/z values of the analytical result are equal so that the peaks overlap.If the m/z values of the two are different, however, the peaks arelocated at the different positions. This difference is a material forjudging the validity of the structure which has been supposed as thecandidate. Here, it is desired that the peak can discriminate whether itis the peaks 5 a and 5 b of the measured values or the peaks of theanalyzed data. This display is exemplified by making so different themode of thickness or color of the line indicating the peaks that may bevisually discriminated.

Moreover, the validity of the structure supposed as the parent ioncandidate 2 a at Step S8 is evaluated, and the result is displayed as anevaluation screen 7, as shown in FIG. 5C. In the evaluation screen 7,there are displayed the parent ion candidate 2 a, a reliabilityindication 7 b and a name 7 c of the sample or the parent ion. Theindication 7 b of the reliability may include not only the percentageindication of the reliability but also a plurality of steps A, B and Catthe reliability levels. Here, the evaluation of the validity means thatthe consistency percentage between the measured value m/z of thedissociated ions and the calculated values of the m/z values of thedissociated ion candidates 5 a and 5 b is calculated so that thecalculation result is indicated as the reliability of the structure ofthe parent ion candidate 2 a supposed in advance. In this example, them/z values of the dissociated ion candidates 5 a and 5 b and theactually measured m/z value of the dissociated ions are consistent sothat the supposed structure of the parent ion has a reliability of 90%.By referring to this evaluation screen 7, the user can confirm not onlythe certainty of the parent ion candidate 2 a supposed but also the nameof the parent ion candidate 2 a. The mass spectrometric data analyzingprocedure in the mass spectrometer 24 is ended by displaying thatevaluation screen 7.

If there are a plurality of candidates for the parent ion, the structureof which is to be supposed at Step S2, for all the parent ioncandidates: the dissociated ion candidates are derived (at Step S5); theanalytical result and the MS² data are compared (at Step S7); and thevalidity of each parent ion is evaluated (at Step S8). The dataprocessing unit 12 derives the consistency percentage or the comparisonresult of the m/z values of the dissociated ions, and the parent ioncandidates to produce those dissociated ions are ranked and displayed inthe order of higher consistency percentages. Here, the consistencypercentages may be indicated either in place of ranks or in numericalvalues together with the ranks.

Without displaying the results (at FIGS. 4B and 4C) of the molecularorbit analysis on the dissociated ion candidates of Step S6, on theother hand, it is arbitrary to display the dissociated ion candidates(i.e., the dissociated ion candidate 5 a and the dissociated ioncandidate 5 b of FIG. 5A) which are finally obtained. In the analyticalresult screen 5, however, there are the results of the thermal, chemicaland energetic calculations and/or the analyzed physical properties.Moreover, the data are desirably saved in files so that the user mayalways peruse and utilize the thermal, chemical and energeticcalculation results for supplying grounds to derive the dissociated ioncandidates. Alternatively, there may be given a function for the user todisplay, if designated. For this file saving, the data are saved in thenot-shown storage device or in a recording medium.

Moreover, the analysis of the mass spectrometric data, i.e., theprocedures from Step S3 to Step S8 has been described such that the massspectrometric data can be analyzed on-site by loading the dataprocessing unit 12 of the mass spectrometer 24 of FIG. 1 with theanalyzing programs. However, the data analysis may also be executed by acomputer disposed separately of the mass spectrometer 24. Here, theapparatus for analyzing the mass spectrometric data is one for makingthe analysis at least on the basis of the mass spectrometric data andfor displaying the analytical result. Therefore, the apparatus isprovided with the data processing unit 12, the display unit 13 and theassociated portion of the control unit 14 as the essential elements, butdoes not always need to be provided with the pretreatment system 8, theionization unit 9, the mass spectrometric unit 10 and the ion detectionunit 11.

According to the present embodiment, the dissociated ions can besupposed highly precisely by calculating at least one of the thermal,chemical energetic properties on the structure of the parent ionsupposed in advance. From these suppositions, the validity of the parention supposed in advance can be evaluated highly precisely to support theidentification of the parent ion or the supposition of the structure ofthe parent ion highly precisely.

By providing the analytical result screen 3 using the display unit 13,moreover, the user is enabled to grasp the analytical result and thedata for the ground easily.

(Second Embodiment)

A second embodiment of the present invention will be described in detailwith reference to the accompanying drawings. The present embodimentrelates to another display method for displaying the analytical resultof the bonding strength a obtained by the molecular orbit analysis byusing the mass spectrometer 24 having the construction shown in FIG. 1.Another example for displaying the bonding strength σ of the parent ion,as derived according to the flow chart of FIG. 2, is exemplified by theranking indications shown in FIG. 6, by the distribution indicationsshown in FIG. 7, by the strength indications by color shown in FIG. 8,or by the symbol indications shown in FIG. 9. Here, the construction ofthe mass spectrometer 24 and the details of the individual steps of FIG.2 are identical to the aforementioned ones of the first embodiment sothat their detailed description will be omitted from the portionsoverlapping the aforementioned embodiment.

FIG. 6 displays a ranking indication screen 14 as an example of theranking indications. The ranking indication screen 14 is constructed tocontain: the structure of the parent ion candidate 2 a; ranking values14 a in which digits indicating the results of the bonding strengthsranked in lower orders are arranged to correspond to the bonds; and atext 14 b for explaining the meanings of the ranking values 14 a.According to this ranking indication screen 14, the breakableness of thebonds can be easily confirmed from the ranking values 14 a. FIG. 6illustrates an example in which digits from “1” to “8” are attached inthe orders of the lower ranks, but all the bonds may be ranked.

FIG. 7 illustrates a distribution indication screen 15 as an example ofthe distribution indication. The distribution indication screen 15 isconstructed to illustrate the locations of atomic bonds of lower bondingstrengths as regions 15 a and 15 b in the stereoscopic structure of theparent ion candidate 2 a, and in addition a text 15 c implying thedistribution indications. The regions 15 a and 15 b are notdiscriminated in FIG. 7, but it can be instantly confirmed that theatomic bonds of the two portions are breakable.

In a strength indication screen 16 illustrated in FIG. 8, on the otherhand, the regions having lower intermolecular bonding forces areillustrated as regions 16 a and 16 b in the parent ion candidate 2 a,and the regions 16 a and 16 b are differently colored according to thebonding strengths so that they may be easily discriminated. In thisstrength indication screen 16, there is arranged a scale 16 c indicatingthe correspondences between the bonding strengths and the colors so thatthe regions of the lower bonding strengths and their strength relationscan be easily confirmed. FIG. 8 illustrates an example indicated atseven stages, which may be differentiated in colors of more or lessstages. In one coloring example, the colors are stepwise changed from ared color indicating the weakest bonding through a green color to a bluecolor indicating a strong bonding, but the coloring may be changed bythe section of the user. Moreover, the regions 16 a and 16 b may besmeared away or may be colored only on contours. The density may be usedin place of or together with the smear-away.

FIG. 9 illustrates a symbol indication screen 17 indicating the bondingstrength with symbols. For the parent ion candidate 2 a, the symbolindication screen 17 contains symbols 17 a and 17 b attached to atomicbonds of lower bonding strengths, and a text 17 c indicating that thebonds bearing the symbols 17 a and 17 b are portions of weak bonds.According to this symbol indication screen 17, the portions of weakbonds can be instantly confirmed. Here, the symbols 17 a and 17 b have atriangular shape but may have another polygon or an arrow. By theaforementioned coloring, moreover, the bonding strength can also beconfirmed.

In addition to the fact that the structure of the parent ion can beidentified highly reliably, according to the present embodiment, thereis obtained an effect that the magnitude relations or strengths of thethermal, chemical and energetic properties can be sensed by using thevarious indications even in case the thermal, chemical and energeticproperties obtained by the molecular orbit analysis are invisible ifdigitally indicated. This effect is prominently exhibited in case theparent ion candidate 2 a to be supposed is composed of many atoms.

Here, FIG. 7 to FIG. 9 have only two indication portions, but one orthree or more indications may be selected according to the kind of thesample or by the selection of the user. Moreover, the number of ranks tobe indicated can also be changed by the selection of the not-shown inputmeans. The ranking indication screen 15 of FIG. 7 and the symbolindication screen 17 of FIG. 9 can attain similar effects even if itsindications are made not in the bond-breakable order but in the order ofthe stronger bonding force. For this case, it is desired that the texts14 b and 17 c contain such indications in addition to the informationindicating the ranking kind as make it possible to discriminate whetherthe orders are in the stronger bonding force or in the weaker bondingforce.

(Third Embodiment)

A third embodiment of the present invention will be described in detailwith reference to the drawings.

The present embodiment is characterized by calculating an activationenergy as the thermal, chemical and energetic properties to be derivedby the molecular orbit analysis, thereby to derive and display thedissociated ions. The data measurement and processing are done by themass spectrometer 24 shown in FIG. 1, and the portions to overlap thoseof the foregoing embodiments will be omitted on their detaildescription.

The procedure for the parent ion to be dissociated into a plurality ofions will be described from the thermodynamic viewpoints. The parent ionseems to be dissociated after it has transited from a stable state to anactive state, and the dissociated ions seem to transit to a stablestate. In the present embodiment, therefore, the dissociated ions arederived (at Step S5) by calculating the energy (i.e., the activationenergy) necessary for the parent ion to transit to the active state inthe molecular orbit analysis of Step S3 of FIG. 2.

FIG. 10 illustrates the result that the dissociated species were derivedby calculating the energy (or the activation energy) necessary for apesticide such as tebufenozide to transit actually to the active stateby the molecular orbit analysis. The tebufenozide 21 a in the stablestage is caused to transit the tebufenozide 21 b in the active state bythe energy from the outside. The tebufenozide 21 b at this time isdissociated, that is, transits to the stabler state or the state of thedissociated ions. The activation energy at this time has a value of 2.17eV, and the energy from the outside is given by the collision against aninert gas or the irradiation with an infrared ray, for example. Thereason why only one dissociated species 22 is illustrated in FIG. 10 isthat the ion species measured by the mass spectrometer 24 as the ionspecies are only the ions of the dissociated species 22 of m/z=297 amongthe molecules obtained by the dissociative reaction.

Moreover, some substance may have different dissociation procedures forone sample. In other words, different dissociated species may beproduced with different activation energies. This case will be describedwhen the parent ion candidate supposed at Step S2 of FIG. 2 is thereserpine 23 having a structure shown in FIG. 11.

The dissociation procedure is examined by analyzing the molecular orbitof the reserpine 23 at Step S3 to calculate the activation energy forthe dissociation. The examination reveals the presence of both thedissociation procedure (as indicated at (1) in FIG. 11) to be excitedwith an energy of about 4 eV and the dissociation procedure (asindicated at (2) in FIG. 11) to be excited with an energy of about 6 eV.Here in the dissociation procedure (1), the C—O—C bonds are broken toproduce dissociated species 24 a and 24 b. When the reserpine 23 isionized, the atoms located near its center are charged so that thedissociated ion candidate derived at Step S5 is the ions of thedissociated species 24 b having an m/z value of 397 amu. In thedissociation procedure (2), on the other hand, the benzene ring ispartially broken to produce dissociated species 25 a and 25 b so thatthe dissociated species 25 b having an m/z value of 448 amu are thedissociated ion candidates.

By thus using the molecular orbit analysis, it is easily understood thata plurality of dissociated species can exist for one sample, and thedissociated species to easily appear can be determined from themagnitude relations of the activation energy. Specifically, it is foundthat the dissociated species to be produced from the reserpine 23 shownin FIG. 11 are the active species 24 b and 25 b, and that the ions ofthe dissociated species 24 b obtained through the dissociation procedure(1) of the lower activation energy have a higher probability ofdetection (or a higher probability of appearance) than that of the ionsof the dissociated species 25 b obtained through the dissociationprocedure (2).

The comparison at Step S7 between the dissociated ion candidate and themass spectrometric data 1 of the dissociated ions measured actually ismade by comparing the mass spectrum made from the m/z value of thedissociated ion candidate and the mass spectrum of the measureddissociated ions.

FIG. 12A illustrates the MS data 1 a of the sample (having an m/z=609amu) or the parent ion actually measured, and FIG. 12B illustrates theMS² data 1 b of the dissociated ions of the sample. The resultsaccording to FIG. 12B are that the dissociated ions have mass spectrumwith peaks at m/z values of 397 amu and 448 amu, and that thedissociated ions having the m/z value of 397 amu have a higher signalintensity than that of the dissociated ions having the m/z value of 448amu, that is, are more dissociable. This result well coincides with theresult of the molecular orbit analysis, as has been described withreference to FIG. 11. From these results, the dissociated ions can bepredicted highly precisely to make a high contribution to thesupposition of the structure of the parent ion, by calculating andderiving the activation energy by the molecular orbit analysis, byderiving the dissociated ion candidate resultantly, and by estimatingthe probability of appearance of the candidate.

(Fourth Embodiment)

A fourth embodiment of the present invention will be described indetail.

The present embodiment will be described on the case, in which themolecular orbit is calculated as the thermal, chemical and energeticproperties to be derived by the molecular orbit analysis or in which thestatic potential distribution or the charge distribution in the neutralstate is calculated. The data measurement and processing are done by themass spectrometer 24 shown in FIG. 1, and the portions to overlap thoseof the foregoing embodiments will be omitted on their detaildescription.

In the case of calculating the molecular orbit, the highest occupiedmolecular orbit (HOMO) and the lowest unoccupied molecular orbit (LUMO),and/or the molecular orbits of their peripheries are calculated to judgethe bonding states of the entire molecule. Here, the HOMO is themolecular orbit, which is occupied by electrons at the highest energylevel, and is an important analytic item for the thermochemicalreaction. On the other hand, the LUMO is the molecular orbit, which isoccupied by electrons at the lowest energy level, and is an importantanalytic item for a reaction (e.g., an optically excited reaction) of aslightly higher energy than that of the thermochemical reaction. Bycalculating the HOMO or LUMO, the unbondably strong portion of theentire molecule can be derived to derive the dissociated species highlyprecisely. By comparing the m/z values of the dissociated species thusderived with the measured value, moreover, the structure of the parention can be supposed highly precisely.

When the static potential distribution, the charge distribution in theneutral state or the distribution of the HOMO is to be calculated, onthe other hand, it is possible to derive the portion which is easilysusceptible to influences at the time of ionizing the parent ioncandidate. For example, the portion where the positively charged atomsH⁺, Na⁺ or Li⁺ are the most bondable is derived in the case of the plusionization, and the portion for the protons to be most dissociable isderived in the case of the minus ionization. FIG. 13 illustrates anexample in which the most bondable portion of protons (H⁺) is displayedas the region 26. According to the present embodiment, the parent ionstructure in the ionized state can be supposed to add the influences onthe dissociation procedure in the ionized state, so that the dissociatedion candidates can be derived highly precisely. By comparing the m/zvalues of the dissociated ion candidates thus derived with the massspectrum of the mass spectrometric data 1 a measured, moreover, thestructure of the parent ion can be supposed highly precisely.

Here, the dissociation procedures, the activation energies, the parention candidates 21 a and 23, the dissociated ion candidates 22, 24 b and25 b and the m/z values, as shown in FIG. 10 and FIG. 11, may bedisplayed in one screen so that they may be visually grasped by theuser. The screens displayed in this case correspond to the parent ioncandidate screen (as referred to FIG. 4A) and the analytical resultscreens 3, 4 and 5 (as referred to FIGS. 4B and 4C and FIG. 5A) in theforegoing embodiments.

The molecular dynamic calculations may be done together with or in placeof the molecular orbit calculations. If the molecular dynamiccalculations are used, the optimum structure for minimizing the energycan be derived to derive the dissociated ion candidate of a stablestructure, i.e., the dissociated ions of a high probability ofproduction (or appearance) as the dissociated ion candidates.

In another method for deriving the dissociated ion candidate byexamining the stability, moreover, the energy level in the state afterthe dissociation may be examined. The dissociated ions at the lowerenergy level are the stabler so that they can be thought to have ahigher probability of appearance. In the case of a plurality ofdissociated ion candidates, the dissociated ions can be predicted highlyprecisely by adding the appearance probability thereby to make a highcontribution to the supposition of the structure of the parent ion.

In case the stable state of the dissociated ion candidates is derived,the appearance probability based thereon may be indicated in numericalvalues. In the case of a plurality of dissociation procedures, the valueof the appearance probability may be exemplified by the ratio of theactivation energy, the ratio of the energy calculated by the moleculardynamic calculations, or the value converted from the difference in theenergy level.

(Fifth Embodiment)

A fifth embodiment of the present invention will be described in detailwith reference to the drawings.

As shown in FIG. 14, the present embodiment is characterized by derivingthe stereoscopic structure of a parent ion by molecular kineticcalculations (at Step S2 a) before the thermal, chemical and energeticproperties are calculated and derived by the molecular orbit analysis(at Step S3) of the parent ion candidate 2 a having the structuresupposed at Step S2. Here, the apparatus construction is identical tothat of the mass spectrometer 24 shown in FIG. 1, and the procedureshown in FIG. 14 is also similar but for the molecular kineticcalculations (at Step S2 a). Therefore, the portions to overlap those ofthe foregoing individual embodiments will be omitted on their detaildescription.

The molecular kinetic calculations to be done at Step S2 a of FIG. 14are to calculate the motions of numerous atoms and moleculesconstructing a substance. These calculations can be used to specify thethree-dimensional structure of the sample having a large atomic numbersuch as a high molecule, when the three-dimensional structure is madehighly different in the ambient temperature, the properties (e.g., thehydrophobic nature or the hydrophilic nature) of bases constructing thesample or the like. In FIG. 15, here is illustrated a peptide orangiotensin 30 which is constructed of seven amino acid configurations.These seven amino acids are Arg (arginine), Val (valine), Try(tyrosine), Ile (isoleucine), His (histidine), Pro (proline) and Phe(phenylalanine). The angiotensin 30 having such configurations exists infact as the angiotensin 31 having a circular construction around thehydrophobic base. Thus, the angiotensin 30 of the ideal structure andthe angiotensin 31 of the actual structure are so structurally differentthat they may probably have different dissociable portions. In order toidentify the structure of the parent ion highly precisely by derivingthe dissociated ion candidate and by comparing it with the MS² data,specifically, the actual stereoscopic structure of the parent ioncandidate used for deriving the dissociated ions is desired to change.Therefore, the parent ion can be identified highly precisely by derivingthe stereoscopic structure of the parent ion candidate to be supposed,before the dissociated ions are derived by using the molecular orbitanalysis at Step S3.

Thus, the structure of the parent ion can be identified in a highreliability according to the present embodiment. Especially in case theparent ion is a high molecule such as peptide or saccharides, thestereoscopic structure of the parent ion to be supposed can be derivedhighly precisely to improve the reliability of the dissociated ionsderived thereon.

(Sixth Embodiment)

A sixth embodiment of the present invention will be described in detailwith reference to the drawings.

The present embodiment is characterized in that the mass spectrometry isdone by using a mass spectrometer 41 shown in FIG. 16 while utilizing aclosed database 42 and a public database 44. This procedure follows aflow chart shown in FIG. 17, and the screen shown in FIG. 18 is providedas one example of the processed result. Here, the portions to overlapthose of the foregoing individual embodiments will be omitted on theirdetail description.

The mass spectrometer 41 or the mass spectrometric data analyzingapparatus is enabled, as shown in FIG. 16, by the data processing unit12 on the basis of the arranged mass spectrometric data 1 to retrievethe data and to suppose and enumerate the structure of the parent ion byeither the closed database 42 owned by the mass spectrometer 41 or thepublic database 44 which can be accessed to through an internet 43 andopened. The candidates of single or a plurality of parent ionstructures, which are supposed and enumerated, can be targeted by theinformation processing method such as a database retrieving method, astatistical processing method or a numerical arrangement.

In the analyzing procedure by the data processing unit 12, the structureof the parent ion is supposed at Step S2 on the basis of the massspectrometric data 1 acquired at Step S1 of FIG. 17. At this time, thereis used the aforementioned closed database 42 or public database 44.Then, at least one of the parent ion candidates obtained by the databaseretrieval is processed (at Step S2 a, Step S3 to Step S8) according tothe aforementioned individual embodiments. Then, the validity of thestructure of the parent ion supposed at Step S8 is evaluated anddisplayed, and the three-dimensional structure of the parent ion isderived and displayed at Step S17. Here, the molecular kineticcalculation at Step S2 a is not essential but can be omitted.

In connection with an example of FIG. 18, here will be described thescreen to be used for supposing the structure of the parent ion at StepS2 and the screen to be used for displaying the three-dimensionalstructure at Step S17. Here in FIG. 18, a surface screen 51 enumeratingthe configurations of amino acids in a table and a pop-up screen 56 or ascreen illustrating the three-dimensional structure of Step S17 areillustrated as the screen to be displayed at Step S2.

The surface screen 51 includes: a rank column 52 ranking the structuresof the parent ion by using the public database 44 and the rules ofthumb; a score column 53 indicating the reliabilities of ranks innumerical values; a configuration candidate column 54 indicating theconfigurations of amino acids; and an analytical result column 55indicating the ranks made by the molecular orbit analysis. In case thestructure is to be supposed from the public database 44 or the like, forexample, the amino acid configuration at the first rank of the rankcolumn 52 is the surest structure. From the result of the molecularorbit analysis in the present embodiment, however, it is indicated thatthe amino acid configuration at the fourth rank in the analytical resultcolumn 55 is the most correct structure.

In case numerous candidates are listed up as the parent ion candidates,their reliabilities are usually indicated by scores, which arefrequently based on the rules of thumb. Against the rules of thumb, thesurest one is finally selected from many candidates by the user on thebasis of the expertise. According to the present embodiment, however,even if such many candidates are enumerated, the dissociated ions can betotally derived by the molecular orbit analysis for all the parent ioncandidates or the parent ion candidates of a high rank for thecorrectness. By comparing the result and the mass spectrum of thedissociated ions actually measured, therefore, the consistency orsimilarity of the two can be derived to evaluate the parent ionstructure more precisely. In other words, the parent ion candidatesenumerated can be newly ranked on the basis of the result of themolecular orbit analysis. According to the present embodiment,therefore, it is possible to suppose the parent ion structure moreprecisely or to provide the reliability ranking of the parent ionstructure from the viewpoint of the molecular orbit analysis.

On the other hand, the pop-up screen 56 shown in FIG. 18 displays thethree-dimensional structure for the parent ion structure at the highrank. With this function, the three-dimensional structure analyticalresult can be derived from the mass spectrometric result remarkablyeffectively for the case in which the three-dimensional structure of asynthetic substance or the like is to be confirmed. It is verybeneficial that the three-dimensional structure of a drug having a veryimportant meaning in the analysis of its three-dimensional structure canbe derived inexpensively and promptly from the mass spectrometricresult. Here, FIG. 18 illustrates the three-dimensional structure as thepop-up screen 56 of the surface screen 51, which may be exemplified byanother screen to be displayed together with the surface screen 51.

(Seventh Embodiment)

A seventh embodiment of the present invention will be described indetail with reference to the drawings.

The present embodiment is characterized by performing the massspectrometry by using a mass spectrometer 61 shown in FIG. 19. Theprocedure to be done in this mass spectrometer 61 is followed accordingto any of FIG. 2, FIG. 14 and FIG. 17 so that its description will beomitted. On the remaining items, the portions to overlap those of theforegoing individual embodiments will be omitted on their detaildescription.

The mass spectrometer 61 or the mass spectrometric data analyzingapparatus is characterized by including an ion trap type massspectrometric unit 62 as the mass spectrometric unit. This ion trap typemass spectrometric unit 62 performs the roles of both the massspectrometric unit 10 shown in FIG. 1 and the not-shown dissociationmeans. By trapping only the mass-selected parent ion in the ion trap andby applying and superposing the CID (Collision Induced Dissociation)field having a frequency resonant to the parent ion to the ion trapfield, the parent ion repeats the collisions against the inert gasfilled in the ion trap, so that it is dissociated. The dissociated ionsare subjected to the mass spectrometry in the ion trap massspectrometric unit 62 so that the mass spectrometric data 1 of theparent ion and the dissociated ions are obtained. According to thepresent embodiment, the ion trap type mass spectrometric unit 62performs the roles of both the ion dissociation and the massspectrometry so that the mass spectrometer can be down-sized.

(Eighth Embodiment)

An eighth embodiment of the present invention will be described indetail with reference to the drawings.

The present embodiment is characterized in that the mass spectrometry isdone by using a mass spectrometer 71 shown in FIG. 20 or a massspectrometer 81 shown in FIG. 21. Here, the portions to overlap those ofthe foregoing individual embodiments will be omitted on their detaildescription.

The mass spectrometer 71 or the mass spectrometric data analyzingapparatus is characterized by including an ion trap 72 as thedissociation means and a Time-Of-Flight type mass spectrometric unit 73as the mass spectrometric unit, as shown in FIG. 20. This massspectrometer 71 is optimized, by using the Time-Of-Flight type massspectrometric unit 73 capable of analyzing a high molecule of a largem/z value, for the case in which a living high molecule is a target forthe analysis or in which another high molecule is to be analyzed. As inthe mass spectrometer 81 shown in FIG. 21, moreover, a Q-pole 82 havingfour rod electrodes may be adopted as the dissociation means. As theions pass through the Q-pole 82 in the atmosphere of a high inert gaspressure, they are trapped to produce the dissociation ions as a resultof the collisions against the inert gas. The Q-pole 82 can make theanalysis of a higher sensitivity than that of the ion trap so that it isoptimized for a microanalysis.

By acquiring the mass spectrometric data using the mass spectrometers 71and 81 of the present embodiment and by making analyses having beendescribed in the foregoing individual embodiments, the structure of theparent ion, i.e., the sample can be identified highly precisely.Especially by using the mass spectrometer 81, the structure of theparent ion, i.e., the sample can be identified highly precisely even ifthe target for the analysis is a high molecule such as protein, peptideor saccharides.

(Ninth Embodiment)

A ninth embodiment of the present invention will be described in detailwith reference to the drawings.

The present embodiment relates to a solution offering system forperforming the analyzing procedure of the foregoing individualembodiments in response to a request from a customer.

As shown in FIG. 22, the solution offering system is realized by amolecular structure solution service offering agency 91. Experts onmolecular orbit analyses and molecular kinetic calculations work at themolecular structure solution service offering agency 91. This agency 91is constructed to include at least the data processing unit 12 and thedisplay unit 13 (as referred to FIG. 1 and so on) and to output thevarious analyzing procedures and the outputs of the analytical resultsin response to the input of the mass spectrometric data 1.

In the solution offering system, the molecular structure solutionservice offering agency 91 evaluates the parent ion structure inresponse to a request of a customer 92 for the structure analysis of asample by the mass spectrometric data analyzing method described in theaforementioned individual embodiments, and offers the finally derivedparent ion structure as the solution to the customer. The structure ofthe parent ion is derived in the molecular structure solution serviceoffering agency 91: by receiving the mass spectrometric data 1 of theparent ion and the dissociated ions, if any, from the customer; byderiving the dissociated ion candidates by the molecular orbit analysesof the parent ion candidates; and by comparing the dissociated ioncandidates and the actually measured mass spectrometric data 1 toidentify the structure of the parent ion. On the other hand, thecustomer requests, if having failed to own the mass spectrometric data1, the agency having the mass spectrometer for the mass spectrometry. Onthe basis of the data obtained by the agency, the molecular structuresolution service offering agency 91 derives the parent ion structure bythe mass spectrometric data analyzing method using the molecular orbitanalysis, and offers the finally identified parent ion structure to thecustomer. On the other hand, the molecular structure solution serviceoffering agency 91 receives, if provided with an apparatus such as themass spectrometer 24 of FIG. 1, a sample in response to a request andperforms the mass spectrometry and the analysis of the massspectrometric data so that it can offer the finally identified parention structure to the customer 92.

Upon offer of the solution, the molecular structure solution serviceoffering agency 91 charges the customer 92. The charged sum is variedfor the case of only the analysis of the mass spectrometric data or forthe case of the additional mass spectrometry, and is determinedaccording to the sample number or the time period for the analysis.

When the request for the structural analysis from the customer 92 isreceived through the network such as the internet, on the other hand,the offer of the solution or the analytical result or the charge for theoffer can also be done through the network.

According to the present embodiment, the experts on the molecular orbitanalyses, molecular dynamics and molecular kinetic calculations can berequested for the evaluation/derivation of the parent ion structure sothat the result derivations of higher precision and reliability can beexpected. Moreover, the work of the customer 92 or the requester can bemade efficient by requesting the external agency for the specialmeasurements and the analyzing works.

Moreover, the present invention should not be limited to theaforementioned individual embodiments but could be widely applied.

For example, the mass spectrometric units 10 and 73 of the massspectrometers 24, 41, 61, 71 and 81 may perform two or moredissociations on the sample. Specifically, the mass spectrometry may bedone by dissociating the once dissociated ions produced from the parention. In this case, the mass spectrometric data (i.e., MS³ data, MS⁴data, - - - , and MS^(n) data, of which letter n designates a positiveinteger 3 or more) of the dissociated ions produced by the second andsubsequent dissociations can be acquired to provide information onsupposition of the structure of a high-molecular sample or the movingstate reaction of a medicine. As the data, there may be acquired either:the MS data 1 a of the case of no dissociation, as illustrated in FIG.3A, and the tandem mass spectrometry (MS^(n): letter n designates aninteger of 2 or more) in which the dissociation procedures are done byan arbitrary number of times; or the data of all dissociation stagesfrom the MS data 1 a to an arbitrary MS^(n) data.

In the case of the structural analysis of a sample or such a protein aswill acquire the intrinsic function when modified by phosphating it orby adding fatty acid or saccharides, moreover, the modification radicalsand the kinds of modifications can be judged by comparing the massspectrometric data when modified and unmodified, to examine the massincrease due to the modifications. In this case, the mass spectrometryneed not be actually done when the mass without the modification can beeasily supposed. However, it is also possible to compare the modifiedsample and the unmodified sample by the individual mass spectrometries,as will be described in the following. When the sample is whollymodified and added, an unmodified sample is prepared by breaking aspecific portion of the modified protein with enzymes. Then, themodified sample and the unmodified sample are subjected as theindividual parent ions to the mass spectrometry thereby to acquire atleast the MS data and the MS² data. On the unmodified parent ion, thedata processing unit 12 analyzes the structure in accordance with theaforementioned individual embodiments and compares the MS data of thetwo parent ions thereby to specify the modifying radicals. At this time,it is desired to examine whether or not the modifying radicals arebonded to the dissociated ions, too, by comparing the corresponding MS²data. The analytical results are displayed in the display unit 13. Thedisplays can be exemplified by the structure of the sample containingthe modifying radicals and/or the structure of the dissociated ionscontaining the modifying radicals.

In another mode of the solution offering service to be done in the ninthembodiment, moreover, the database of the MS^(n) data, which has beenderived by the molecular orbit calculations from the molecular structuresolution service offering agency 91, is offered to the customer 92. Thisdatabase has a structure in which the names, the m/z values, thestructures and the physical properties of samples and bases described inthe aforementioned individual embodiments are so configured at leastpartially that they can be retrieved.

Moreover, it is also contained in the execution of the present inventionto analyze the structure of the sample by causing a computer having atleast data processing function to start the analyzing program for theanalyzing procedures described in the aforementioned individualembodiments, and to record such analyzing program in a recording mediumsuch as the CD-ROM or to transmit the program through the network.

According to the present invention, it is possible to derive thestructure of a sample highly precisely. By offering the result and thegrounding for the derivation by a screen display, moreover, it ispossible to confirm and utilize the analytical result efficiently.

1. A mass spectrometer for analyzing the structure of a samplecontaining protein, peptide, saccharide or a complex compound of peptideand saccharide, the mass spectrometer comprising: an ionization unit forionizing said sample; a measuring unit for measuring a property of thesample ionized by said ionization unit; an operation unit for operatingat least one of a thermal property, a chemical property and an energeticproperty calculated by a molecular orbit analysis of a candidate of thestructure of said ionized sample; and an evaluation unit for evaluatingthe validity of the candidate of the structure of said ionized sample onthe basis of said at least one property of the sample measured by saidmeasuring unit and the property of the candidate of the structure ofsaid ionized sample.
 2. A mass spectrometer for analyzing the structureof a sample containing protein, peptide, saccharide or a complexcompound of peptide and saccharide according to claim 1, wherein said atleast one of a thermal property, a chemical property and an energeticproperty calculated by a molecular orbit analysis is interatomic bondstrength, the reactivity or activation energy, charge distribution orstatic potential in a neutral state.
 3. A mass spectrometry method foranalyzing the structure of a sample containing protein, peptide,saccharide or a complex compound of peptide and saccharide, the methodcomprising: ionizing said sample; measuring a property of the sampleionized by an ionization unit; operating at least one of a thermalproperty, a chemical property and an energetic property calculated by amolecular orbit analysis of a candidate of the structure of said ionizedsample; and evaluating the validity of the candidate of the structure ofsaid ionized sample on the basis of the property of the sample measuredby said measuring unit and said at least one property of the candidateof the structure of said ionized sample.
 4. A mass spectrometry methodfor analyzing the structure of a sample containing protein, peptide,saccharide or a complex compound of peptide and saccharide, according toclaim 3, wherein said at least one of a thermal property, a chemicalproperty and an energetic property calculated by a molecular orbitanalysis is interatomic bond strength, the reactivity or activationenergy, charge distribution or static potential in a neutral state.